Job ID = 14172192 SRX = SRX9427695 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14163757 spots for SRR12975502/SRR12975502.sra Written 14163757 spots for SRR12975502/SRR12975502.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172669 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:08 14163757 reads; of these: 14163757 (100.00%) were unpaired; of these: 6482329 (45.77%) aligned 0 times 2052241 (14.49%) aligned exactly 1 time 5629187 (39.74%) aligned >1 times 54.23% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2296752 / 7681428 = 0.2990 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 14:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 14:52:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:52:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:52:35: 1000000 INFO @ Sat, 11 Dec 2021 14:52:40: 2000000 INFO @ Sat, 11 Dec 2021 14:52:45: 3000000 INFO @ Sat, 11 Dec 2021 14:52:51: 4000000 INFO @ Sat, 11 Dec 2021 14:52:56: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 14:52:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:52:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:52:58: #1 total tags in treatment: 5384676 INFO @ Sat, 11 Dec 2021 14:52:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:52:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:52:58: #1 tags after filtering in treatment: 5384676 INFO @ Sat, 11 Dec 2021 14:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:52:58: #1 finished! INFO @ Sat, 11 Dec 2021 14:52:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:52:59: #2 number of paired peaks: 5529 INFO @ Sat, 11 Dec 2021 14:52:59: start model_add_line... INFO @ Sat, 11 Dec 2021 14:52:59: start X-correlation... INFO @ Sat, 11 Dec 2021 14:52:59: end of X-cor INFO @ Sat, 11 Dec 2021 14:52:59: #2 finished! INFO @ Sat, 11 Dec 2021 14:52:59: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 14:52:59: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 14:52:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.05_model.r WARNING @ Sat, 11 Dec 2021 14:52:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:52:59: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 14:52:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:52:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 14:52:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:52:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:53:05: 1000000 INFO @ Sat, 11 Dec 2021 14:53:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:53:12: 2000000 INFO @ Sat, 11 Dec 2021 14:53:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:53:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:53:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.05_summits.bed INFO @ Sat, 11 Dec 2021 14:53:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9198 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:53:18: 3000000 INFO @ Sat, 11 Dec 2021 14:53:24: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 14:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 14:53:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:53:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:53:31: 5000000 INFO @ Sat, 11 Dec 2021 14:53:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:53:33: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:53:33: #1 total tags in treatment: 5384676 INFO @ Sat, 11 Dec 2021 14:53:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:53:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:53:33: #1 tags after filtering in treatment: 5384676 INFO @ Sat, 11 Dec 2021 14:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:53:33: #1 finished! INFO @ Sat, 11 Dec 2021 14:53:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:53:34: #2 number of paired peaks: 5529 INFO @ Sat, 11 Dec 2021 14:53:34: start model_add_line... INFO @ Sat, 11 Dec 2021 14:53:34: start X-correlation... INFO @ Sat, 11 Dec 2021 14:53:34: end of X-cor INFO @ Sat, 11 Dec 2021 14:53:34: #2 finished! INFO @ Sat, 11 Dec 2021 14:53:34: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 14:53:34: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 14:53:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.10_model.r WARNING @ Sat, 11 Dec 2021 14:53:34: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:53:34: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 14:53:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:53:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:53:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:53:36: 1000000 INFO @ Sat, 11 Dec 2021 14:53:42: 2000000 INFO @ Sat, 11 Dec 2021 14:53:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:53:49: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:53:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:53:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:53:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.10_summits.bed INFO @ Sat, 11 Dec 2021 14:53:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3177 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:53:55: 4000000 INFO @ Sat, 11 Dec 2021 14:54:01: 5000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:54:04: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:54:04: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:54:04: #1 total tags in treatment: 5384676 INFO @ Sat, 11 Dec 2021 14:54:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:54:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:54:04: #1 tags after filtering in treatment: 5384676 INFO @ Sat, 11 Dec 2021 14:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:54:04: #1 finished! INFO @ Sat, 11 Dec 2021 14:54:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:54:05: #2 number of paired peaks: 5529 INFO @ Sat, 11 Dec 2021 14:54:05: start model_add_line... INFO @ Sat, 11 Dec 2021 14:54:05: start X-correlation... INFO @ Sat, 11 Dec 2021 14:54:05: end of X-cor INFO @ Sat, 11 Dec 2021 14:54:05: #2 finished! INFO @ Sat, 11 Dec 2021 14:54:05: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 14:54:05: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 14:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.20_model.r WARNING @ Sat, 11 Dec 2021 14:54:05: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:54:05: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 14:54:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:54:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:54:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:54:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:54:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427695/SRX9427695.20_summits.bed INFO @ Sat, 11 Dec 2021 14:54:21: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (865 records, 4 fields): 3 millis CompletedMACS2peakCalling